Expanding The Known Diversity And Environmental Distribution Of An Uncultured Phylogenetic Division Of Bacteria

Expanding the Known Diversity and Environmental Distribution of an Uncultured Phylogenetic Division of Bacteria
Downloaded from http://aem.asm.org/ on August 15, 2012 by UNIV DE LOS ANDES ILS MEDICINA Michael A. Dojka, J. Kirk Harris and Norman R. Pace Appl. Environ. Microbiol. 2000, 66(4):1617. DOI: 10.1128/AEM.66.4.1617-1621.2000.

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APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 2000, p. 1617–1621 0099-2240/00/$04.00 0 Copyright © 2000, American Society for Microbiology. All Rights Reserved.

Vol. 66, No. 4

Expanding the Known Diversity and Environmental Distribution of an Uncultured Phylogenetic Division of Bacteria
MICHAEL A. DOJKA,† J. KIRKHARRIS,
AND

NORMAN R. PACE*

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
Received 29 November 1999/Accepted 23 January 2000

Downloaded from http://aem.asm.org/ on August 15, 2012 by UNIV DE LOS ANDES ILS MEDICINA

Culture-independent molecular phylogenetic methods were used to explore the breadth of diversity andenvironmental distribution of members of the division-level “candidate” phylogenetic group WS6, recently discovered in a contaminated aquifer and with no cultivated representatives. A broad diversity of WS6affiliated sequences were cloned from 7 of 12 environments investigated: mainly from anaerobic sediment environments. The number of sequences representing the WS6 candidate division was increased from 3to 60 in this study. The extent of phylogenetic divergence (sequence difference) in this candidate division was found to be among the largest of any known bacterial division. This indicates that organisms representing the WS6 phylogenetic division offer a broad diversity of undiscovered biochemical and metabolic novelty. These results provide a framework for the further study of these evidentlyimportant kinds of organisms and tools, the sequences, with which to do so. Perspective on the extent of bacterial diversity has expanded substantially in the past decade. In 1987, Woese could describe 12 main relatedness groups comprising the domain Bacteria, using 16S rRNA oligonucleotide catalogs and the few continuous 16S rRNA sequences then available (12). These relatedness groups have beentermed “kingdoms,” “phyla,” or “divisions,”. We use the term “division” to describe a phylogenetic relatedness group of 16S rRNA sequences that are reproducibly monophyletic and unaffiliated with all other deepest branchings in the bacterial tree. Application of rapid sequencing techniques to cloned 16S rRNA genes from cultures, and especially to environmental samples, has revealed substantialadditional diversity beyond the 12 divisions described by Woese (11). Currently, 36 to 38 phylogenetic divisions of Bacteria are indicated by analysis of ca. 15,000 rRNA sequences from cultured and environmental organisms (5). Thirteen of those phylogenetic divisions have only been encountered in sequence-based environmental surveys and currently have no cultivated representatives. Some sequence-definedphylogenetic divisions are represented by only a few ( 10) sequences, so the extents of diversity within the clades are unknown. Recent studies have found that representatives of bacterial divisions with few or no cultivated members are widely distributed in the environment and numerically seem to dominate many of the environments examined. Specifically, members of the bacterial divisions...